CAREER: Designing Systems for Molecular Query-Retrieval and Molecular Informatics

管理和有效推理分子结构信息的能力对生物化学研究以及发现新的更有效的治疗方法都有巨大的影响。核磁共振、晶体学和组合化学等技术的出现，使我们今天能够在分子结构水平上产生前所未有的大量信息。然而，生成分子结构数据的能力远远超过了我们有效管理、查询和吸收最新技术的能力。从计算机科学的角度来看，分子是复杂的、多维的实体，它对表示、检索、建模和交互技术的有效和高效设计提出了严峻的挑战。在此背景下，本研究主要关注三个挑战：(1)设计基于分子表示和相似性的匹配技术；(2)开发用于分子查询检索的索引策略；(3)设计用于发现治疗方法的知识环境。具体的研究创新包括设计标准坐标系统来表示高度复杂的分子表面，开发用于比较分子的有效信息匹配和检索技术，以及设计分子结构和生物特性的集成信息管理，包括开发用户数据交互技术和上下文支持访问元知识的算法。更广泛的影响：作为本研究的一部分开发的技术和系统将公开可用，并允许在分子信息的管理、探索、分析和推理方面取得根本性的进步。这有可能在药物/治疗发现等领域带来突破性进展，因此对整个社会至关重要。此外，本研究将使“分子查询-检索与分子信息学”成为信息管理、检索、分析和同化等计算机科学研究的重要组成部分。这将允许计算机科学家参与和推进一个关键的和新的跨学科领域。最后，教育和外展部分将(a)开发模型以提高学生的研究经验和生产力，(b)通过与K-12年级的学生和教师进行新颖的互动，在基层提供接触计算机科学的机会，以及(c)通过指导妇女和少数民族学生扩大参与。

The ability to manage and efficaciously reason with molecular structural information has enormous impact both for bio-chemical research as well as for the discovery of new and more efficacious therapeutics. The advent of technologies like NMR, Crystallography, and Combinatorial Chemistry, allow us today to generate unprecedented amounts of information at the molecular structural level. However, the capacity to generate molecular structural data far exceeds our ability to effectively manage, query, and assimilate it at the state-of-the-art.From a computer science perspective, molecules are complex, multidimensional entities which present critical challenges for effective and efficient design of representation, retrieval, modeling, and interaction techniques. In this context, this research focuses on three challenges: (1) Designing techniques for representation and similarity-based matching of molecules, (2) Development of indexing strategies for molecular query-retrieval, and (3) Designing knowledge environments for discovery of therapeutics. The specific research innovations include design of standard coordinate systems to represent highly complex molecular surfaces, developing efficient information matching and retrieval techniques for comparing molecules, and design of integrated information management of molecular structures and biological properties including the development of user-data interaction techniques and algorithms for context supportive access to meta-knowledge. Broader Impact: Techniques and systems developed as part of this research will be made publicly available and allow fundamental advancements in management, exploration, analysis, and reasoning with molecular information. This has the potential to introduce ground breaking advancements in areas like drug/therapeutics discovery and thus is critical to the society at large. Furthermore, this research will establish "Molecular Query-Retrieval and Molecular Informatics" as an integral part of computer science research in information management, retrieval, analysis, and assimilation. This will allow computer scientists to participate and advance a critical and new interdisciplinary area. Finally, the education and outreach component will (a) develop models to enhance research experience and productivity of students, (b) providing exposure to computer science at the grassroots-level through novel interactions with students and teachers at K-12 levels, and (c) broaden participation by mentoring women and minority students.